The Japanese assumptions about Black people were generally learned behavior from witnessing the Europeans treatment of them. Showing Europeans in Japan in 1600 wothout Black people is a distortion of history.

Yasuke was an exception to the rule and Black people were extremely rare when he was in Japan (before Shogun was set). There was no suggestion Yasuke should have been shown, though there was a flashback scene where he might have been present had the screenplay went in that direction.